relax SVN archive

Added NMR library function to convert the given frequency from rad/s to ppm units.

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

Added an intermediate attempt to show the back_calculated data in the graph for R1rho R2 as function of the effective field in rotating frame: w_eff.

The graph is aiming for the representation of Figure 2 in Kjaergaard et al 2013. (http://dx.doi.org/10.1021/bi4001062).
The figure can be seen at https://gna.org/support/download.php?file_id=20208.

It becomes clear, that it is not neccessary interpolate through the spin-lock offset, but it is suffucient to interpolate through the spin-lock field strengths.
The necessary step was the extraction of the effective effective field in rotating frame, w_eff.

In earlier attempt is shown at:
http://wiki.nmr-relax.com/File:Matplotlib_52_N_R1_rho_R2eff_w_eff.png

This though show lines for 6 offset values.
The question is how to show the single line of interpolation.

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

Added the the back_calculated R_2 as function of effective field in rotating frame: w_eff.

R1rho R_2 is defined as:
R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho - R_1 * cos^2(theta) ) / sin^2(theta)

This is described more at:
http://wiki.nmr-relax.com/DPL94#Equation_-_re-writed_forms

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

Some Python 3 fixes as identified by the 2to3 script.

Some changes as identified by the Python 2 to 3 upgrade script /usr/bin/2to3.

Deleted the ancient optimisation_testing.py script, as this no longer works and is of no use.

Updated the frame order optimisation results for the 2nd CaM rotor test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.

Merged revisions 24739-24743,24751-24752 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24739 | bugman | 2014-07-25 12:14:00 +0200 (Fri, 25 Jul 2014) | 21 lines

Reverted r24024, the deletion of the Relax_disp.test_hansen_cpmg_data_to_lm63_3site system test.

See the thread at http://thread.gmane.org/gmane.science.nmr.relax.scm/21774/focus=6300 for the
request that this deletion be reverted. This is the only system test for the 'LM63 3-site'
dispersion model using real data. Having this test allows for better coverage of the code.

The command used was:
svn merge -r24024:r24023 .

.....
r24024 | tlinnet | 2014-06-17 12:32:34 +0200 (Tue, 17 Jun 2014) | 4 lines
Changed paths:
M /trunk/test_suite/system_tests/relax_disp.py

Removed systemtest test_hansen_cpmg_data_to_lm63_3site.

This was a temporary implementation and has been replaced with systemtest:
Relax_disp.test_lm63_3site_synthetic
.....
........
r24740 | bugman | 2014-07-25 12:14:44 +0200 (Fri, 25 Jul 2014) | 5 lines

Updated the Relax_disp.test_hansen_cpmg_data_to_lm63_3site system test.

This is for the changes to the optimisation user functions.
........
r24741 | bugman | 2014-07-25 12:18:44 +0200 (Fri, 25 Jul 2014) | 6 lines

Updated the checks in the Relax_disp.test_hansen_cpmg_data_to_lm63_3site system test.

The values were incorrect due to a bug in relax and a non-optimal minfx setting
(https://gna.org/bugs/?22210 and https://gna.org/bugs/?22211).
........
r24742 | bugman | 2014-07-25 13:35:34 +0200 (Fri, 25 Jul 2014) | 7 lines

Fix for a fatal bug for the prompt UI on MS Windows.

The improvements in the tab completion support for the prompt UI on Mac OS X systems (r24421) was
fatal for certain Python readline modules on MS Windows, as readline.__doc__ can be None. This is
now correctly handled.
........
r24743 | bugman | 2014-07-25 13:39:33 +0200 (Fri, 25 Jul 2014) | 16 lines

Reverted r24736 as this was fatal for the relax information printout - the modules are required.

The command used was:
svn merge -r24736:r24735 .

.....
r24736 | bugman | 2014-07-25 11:20:21 +0200 (Fri, 25 Jul 2014) | 5 lines
Changed paths:
M /trunk/dep_check.py

Clean up of the dep_check module - all imported and unused modules are now deleted as well.

This cleans up the module namespace of the unused imports.
.....
........
r24751 | bugman | 2014-07-25 15:08:57 +0200 (Fri, 25 Jul 2014) | 5 lines

Decreased the precision the Relax_disp.test_hansen_cpmg_data_to_lm63_3site system test.

This is to allow the test to pass on Mac OS X systems.
........
r24752 | bugman | 2014-07-25 15:13:11 +0200 (Fri, 25 Jul 2014) | 7 lines

Unit test fix for Mac OS X.

This is for the test_ns_mmq_2site_korzhnev_2005_15n_dq_data_complex128 test of
test_suite.unit_tests._lib._dispersion.test_matrix_exponential.Test_matrix_exponential. The
tests no longer check for exact values, but use the assertAlmostEqual() calls instead.
........

Unit test fix for Mac OS X.

This is for the test_ns_mmq_2site_korzhnev_2005_15n_dq_data_complex128 test of
test_suite.unit_tests._lib._dispersion.test_matrix_exponential.Test_matrix_exponential. The
tests no longer check for exact values, but use the assertAlmostEqual() calls instead.

Decreased the precision the Relax_disp.test_hansen_cpmg_data_to_lm63_3site system test.

This is to allow the test to pass on Mac OS X systems.